SUMMARY: Investigating crop diversity through genome‐wide association studies (GWAS) on core collections helps in deciphering the genetic determinants of complex quantitative traits. Using the G2P‐SOL project world collection of 10 038 wild and cultivated Capsicum accessions from 10 major genebanks, we assembled a core collection of 423 accessions representing the known genetic diversity. Since complex traits are often highly dependent upon environmental variables and genotype‐by‐environment (G × E) interactions, multi‐environment GWAS with a 10 195‐marker genotypic matrix were conducted on a highly diverse subset of 350 Capsicum annuum accessions, extensively phenotyped in up to six independent trials from five climatically differing countries. Environment‐specific and multi‐environment quantitative trait loci (QTLs) were detected for 23 diverse agronomic traits. We identified 97 candidate genes potentially implicated in 53 of the most robust and high‐confidence QTLs for fruit flavor, color, size, and shape traits, and for plant productivity, vigor, and earliness traits. Investigating the genetic architecture of agronomic traits in this way will assist the development of genetic markers and pave the way for marker‐assisted selection. The G2P‐SOL pepper core collection will be available upon request as a unique and universal resource for further exploitation in future gene discovery and marker‐assisted breeding efforts by the pepper community.

Peppers (Capsicum sp.) are an increasingly important crop because of their use as a vegetable, spice, and food colorant. The oomycete Phytophthora capsici is one of the most devastating pathogens to pepper production worldwide, causing more than $100 million in losses annually. Developing cultivars resistant to P. capsici is challenging because of the many physiological races that exist and new races that are continuously evolving. This problem is confounded by the lack of a universal system of race characterization. As a basis to develop a global anticipatory breeding program, New Mexico recombinant inbred lines (NMRILs) functioned as a host differential for Phytophthora root rot to characterize the race structure of P. capsici populations in Taiwan. Using the NMRILs, 24 new races were identified, illustrating the utility and usefulness of the NMRILs for anticipatory breeding. Virulence of P. capsici was observed to be geographically specific and in two virulence clusters. Interestingly, all but two isolates collected in 2016 were the A2 mating type, which is a shift from the predominantly A1 mating type isolates collected prior to 2008. The NMRILs host differential provides an approach for scientists to work together on a global scale when breeding for resistance as well as on a local level for regional gene deployment. Additionally, we propose that the current race numbering system, which has no biological meaning, be supplemented with the virulence phenotype, based on the susceptible NMRILs to a given isolate. This work provides insights into the population dynamics of P. capsici and interactions within the highly complex Capsicum−Phytophthora pathosystem, and offers a basis for similar research in other crops.

Chile pepper ( Capsicum annuum L.) is an increasingly important vegetable and spice crop. Among the most devastating chile pepper–infecting viruses, especially in tropical and subtropical regions, are members of the whitefly transmitted Begomovirus , which cause pepper yellow leaf curl (PYLC). An effective PYLC management strategy is the development of resistant cultivars. However, genetic recombination, acquisition of extra DNA components, and synergistic interactions among different begomoviruses have resulted in the rapid emergence of new viruses that can infect new hosts, cause new disease symptoms, and overcome host resistance. In this project, 98 Capsicum entries comprising breeding lines, open pollinated varieties, genebank accessions, and wild species were screened for resistance to strains of Pepper yellow leaf curl Thailand virus (PepYLCThV). We used a randomized complete block design with three replications and 10 plants per replication in field net-houses at two locations (Khon Kaen and Kamphaeng Saen, Thailand) using augmented inoculation by viruliferous whiteflies. Scoring was done at ≈60, 90, and 120 days after inoculation using a standardized 6-point scale (1 = no symptoms to 6 = very severe symptoms), and the average of the scores of 10 plants within each replication was used for analysis. Although no entry was immune to the disease, the breeding line 9852-123 was highly resistant. Several accessions and lines were moderately resistant at both locations, although a high level of variability within these entries was observed. Overall, the disease severity at the Khon Kaen location was greater compared with Kamphaeng Saen, highlighting the importance of multilocation testing for disease resistance. The resistant entry identified here can be used to study gene action and to move resistance genes into well-adapted germplasm.

Multilocation trials are important for breeding programs to identify high-yielding, adapted lines for a wide range of environments. In this study, we evaluated yield and yield components (fruit weight, fruit length, and fruit width) as well as days to 50% anthesis and fruit maturity of the 10 chili pepper lines in the International Chili Pepper Nursey 15 (ICPN15) distributed by the World Vegetable Center to interested cooperators worldwide. Performance data of the ICPN15 entries were received from collaborators evaluating the set in seven different environments in five countries (Indonesia, South Korea, Thailand, Taiwan, and Vietnam). Significant genotype-by-environment (G × E) interactions were detected for all traits evaluated. Additive main effect and multiplicative interaction analyses indicated high environmental influence on yield, days to 50% anthesis, and maturity, whereas genotype was the greatest contributor to variability in the market-driven yield components of fruit length, width, and weight. Four lines (ICPN15-4, -5, -7, and -10) were identified as highly stable and could serve as sources of yield and yield component stability in either short fruit market segments (ICPN15-4) or long fruit market segments (ICPN15-5, -7, and -10). We attempted to used publicly available weather data to help in explaining the source of the environmental variability; however, differences between analyzed and observed weather were too different to be useful. This is evidence that weather data should be collected at each testing environment in future studies. This study provides a basis for future studies in the stability of important horticultural traits in pepper, and highlights the need for further work in this area.

Recently, there has been a substantial increase in high‐throughput technologies that generate highly complex large datasets for use in the sciences. Plant breeding and genetics have benefited from this data explosion where many public and private institutions now implement genomic and phenomic data to predict performance thus informing germplasm selection. However, the multitude of methodologies and data generates a situation of strategic uncertainty. We set out to compare different methods of genomic and phenomic selection in the Capsicum core collection, developed through the G2P‐SOL project, producing a combination of unique and similar selected genotypes for heat tolerance. Combined, the methods tested identified a total of 33 genotypes that show tremendous promise for use as parents in heat tolerance breeding: with 13 of these being present in more than 1 selection method. Combining classical and multispectral phenotyping methods produced better selection results than either method alone. When each method was conducted without being informed by the other, similar results were obtained. Our weighted rank‐sum selection index identified 10 entries across environments that show heat tolerance, 8 of which are also selected within heat environments. This suggests that different breeding programs can reach similar results despite having different logistical constraints. Our case study within pepper germplasm using phenomic and genomic data exhibits the potential to compensate for the dearth of germplasm knowledge with high‐throughput data as well as the converse, to compensate for logistical or financial constraint to new technologies with breeder knowledge.